Recent research indicates that human observers can perform high-level cognitive tasks typically associated with working memory processes (e.g. learning of complex item sequences, reading, arithmetic or delayed visual discrimination) independently of conscious awareness of the relevant information. However, the neural basis of this phenomenon is not known. Here we show neuroimaging and neurostimulation evidence that the dorsolateral and anterior prefrontal cortex can operate on non-conscious information in a manner that goes beyond automatic forms of sensorimotor priming and which may support implicit working memory processes and higher-level cognitive function.